Time Lord in Training
by superFREAKINwholock
Summary: A Doctor Who A/U In which it is Dean invites Sam onto his TARDIS to learn the ropes but when they decide to fix her up after a bad crash with Bobby and Castiel, they encounter some aliens which they have never encountered before. But with Castiel and Sam holding dark memories will they be able to overcome the new threats, or will they fail to overcome the threats and themselves?
1. Chapter 1

**A/N Hi! This is a Supernatural/DoctorWho crossover. I don't have a definite clue on how many chapters it will be, only that it will over five. Please tell me your opinions in the review section; I would like to know what you think. **

**I am co-writing a superwholock piece with my cousin ImpalaTardis (who is amazing) called Politically Incorrect, it's about the government being taken over by demons, also enjoy the unlikely bromance **

**Enjoy :D x**

"This is my baby, Sammy. I'm only two regenerations from the limit and I want someone I trust to take her on, and that person is you!" Dean gestured to a tall blue police box across the road through a heavy sheet of rain, "One day you will be in charge of her and be a Time Lord like me, but for now your job is to follow my instructions."

Sam smiled; he always wished that he could follow his brother through the ranks and join him as a Time Lord.

The rain started to lash down on the pair so Dean decided to cross the road back to his beloved time machine. He looked left then right before crossing the road quickly and heading to the TARDIS, shoving people out the way and leaving Sam to say sorry.

Fiddling for his keys, Dean finally fished them out of his pocket with shaking hands and tried to put the key into the door.

It didn't work.

He swore.

"Are you sure this is your TARDIS?" Sam questioned sarcastically.

Dean scowled at him, "Yes. I would know my baby anywhere. Now let's try again."

Dean tried again but to no avail.

"Damn it, Cas!" He exclaimed, thumping the door in anger.

"Who?" Queried Sam, not quite understanding.

He muttered something under his breath.

Then the TARDIS door opened.

A man with dark brown hair, blue eyes and a trench coat looked down at them from his aggressive stance in the doorway, blocking the two brothers' view of anything on the inside. The man glared down at the pair, squinting threateningly, before smiling sweetly.

"You… You… You changed the stupid locks! Not cool! You're not supposed to do that! The last time that you did that I almost got skinned by a Slitheen! Just let me and Sasquatch in before I gank ya'." Dean threatened while rising onto his toes.

The squinting man backed down and walked to the control panel in the centre of many rooms, leaving an open invitation for Sam and Dean to follow.

Sam stared in awe, the TARDIS was awesome!

The room was covered in classic rock memorabilia from Earth and AC/DC blasted from homemade speakers stationed in everyplace possible. The pillar in the middle of the room was red and black- supposedly Dean had _altered_ it after he _crash_ landed it in the middle of a music festival- and the panels were oddly shaped and coloured, but all Sam wanted to do was push the buttons and drive it.

Dean caught Sam looking at the control panel and he chuckled, "Once you learn the basics I'll let you press the buttons. Don't worry you delicate head, Princess." He joked.

He reached up and ruffled Sam's long hair.

"Remind me to make you a hair cutting appointment, your hair is getting out of control!"

Dean left Sam to his own devices, which mainly consisted of staring in awe at the machines magnificence and strolled over to Cas who was fiddling with the buttons on the panel; the buttons made fart noises.

He sighed and tapped his friend on the shoulder who pointed nonchalantly over to one of the coat racks on the left hand side of the room, back where Dean had just been. The bow legged man sighed and lazily meandered down some steps. With a little jump he grabbed his new set of keys and gave his spare to Sam whom was still staring at the whole thing in awe.

"Look after this Sam. You won't get another one, you hear me? Lose this and I'm taking you right back home." Dean pressed the keys into Sam's palm, "I'm not joking, if you lose this key Castiel will have to make a new lock, which will mean another set of keys, and guess what you won't get another one. All you will get is a ticket back home." He looked into Sam's eyes, "Now keep this safe and don't lose it!"

Sam returned his older brother's stare, "I won't lose it, jerk." He pointed over to Castiel, "Who is your friend over there? I thought you travelled alone?"

Dean sighed, "That's Castiel. He… he… has a difficult past and I would prefer him to tell it rather than me. I don't want to keep things from you, but Castiel's story is better coming from his mouth rather than mine."

Dean looked lost in thought for a moment before snapping back into his normal self.

"Let's introduce you to the crew!"Dean put his arm around Sam and dragged him to the control panel where Cas was logging the farts of the slitheen in to the TARDIS and making sure that the TARDIS would alert them if it heard one.

"Cas?" Dean said in an assertive tone.

No response.

"Cas?" he tried again louder.

The man known as Cas looked like a deer in the headlights and shot into a standing position quickly, but not before banging his head. He looked to Sam.

"Hello Sam. I am Castiel." He said in monotone.

He held out a hand expecting it to be shaken.

Sam took the hand gingerly and replied nervously, "Hey, Castiel."

Dean slapped Sam's back in a brotherly way.

"Right! Now the introductions are finished with, I shall go out and find some pie!" Dean sauntered out the door purposely with some dollars in his pocket to find the nearest place to buy some pie.

Castiel watched Dean walk out the door, _Now I have to make use of my limited _people skills _many of which are _rusty_. Thank you, Dean._

Castiel tapped a button on the panel and the music stopped playing. He then walked past Sam who followed his every move. He bent down into a little cubby how under the panel and pulled out two steaming mugs of coffee and offered one to Sam. When Sam declined he awkwardly put the mug back where it came from. He dove in again and pulled out a burger. He again offered one to Sam who declined, again, and started eating. Standing awkwardly near Sam, he pulled a button on the control panel and the music started up again, but this time it was classical music.

Sam looked around uncomfortably while the music played, looking for a way to start conversation. He put his hands in his pocket and decided that he might as well ask a few questions to ease the tension.

"So you like classical music then… You know I like it too… it's very relaxing…" Sam commented, he desperately wanted Dean to come back.

Castiel nodded and sipped a bit of his coffee before taking a huge bite on his burger.

"Why did Dean have to go out and get pie when there is a food machine in here?" Sam observed looking suspiciously at the device.

Castiel shrugged, "He prefers the taste, though there is no difference. Perhaps he likes it because someone made it lovingly themselves and not by an emotionless machine." He offered, motioning towards the device with his foot.

He then added, after another period of silence, "Why do you want to become a Time Lord?"

"I was a bit reluctant at first but my brother says it's a cool job and he says he has a lot of fun travelling through space and time, so I thought why not." Sam told him straight out.

Castiel glowered at the floor. It looked as though he was trying to burn a hole right through it.

Sam thought he better avoid saying anymore on the subject, so instead he commented on something else.

"Why is your tie on the wrong way 'round?" Sam noted.

Castiel looked down and his face fell, he thought that he had put it on the right way this morning.

"Dean usually does it for me. It seems as if I am incapable of doing ties correctly." He said abashed.

_Better avoid his tie as well. How many sensitive spots does this guy have? _ Sam pondered.

Sam listened to the music playing, he remembered it; it was Mozart 50. He smiled fondly.

"You enjoy Mozart?" Castiel noted, watching Sam's face intently.

"Yeah, Dean took me to see it when I had my first regeneration. It was really good, he didn't enjoy it much."

Sam shuffled over to one of the chairs and sat down heavily. When would Dean get back?

Castiel finished his burger and coffee quickly before pressing the buttons that made farting noises.

Over an hour passed and still Dean had not come home. The awkwardness of the situation had become unbearable and Sam felt that if Dean did not come back, then he would regenerate so they would have something to talk about.

Suddenly the door swung open and Dean sauntered back in with a cocky smile on his face and half a slice of pie in his hands. He took a bite of the pie.

"Did you miss me?" He mumbled through a mouthful of pie. The expressions on Sam and Castiel's faces were full of relief.

Sam rushed in to Dean's arms and put his head on the older brother's head and fiercely whispered, "Do that again and you will die."

Dean laughed and continued up the steps once he had extricated himself from his brother. He then greeted Castiel with a short hi.

He did a double take; Castiel had done his tie wrong again.

Shaking his head he turned off the classical music that was being played and turned towards the two men.

"How awkward was it? On a scale of one to ten, how awkward?" Dean grinned and tapped Cas on the shoulder. He then walked around the back of Castiel and un-did the tie and re did it again.

Sam looked on with confusion, the set up he and Cas had was weird.

"So Larry and Loner aren't going to talk, or shall gue-"

"Eight." Castiel interjected, not wanting Dean to drag it out.

Sliding his hands from around Castiel's shoulders he walked around the panel.

Dean decided to change the subject even though he was having fun.

"Where do you want to go Sammy? You have your pick." He looked towards Sam, who had sat back down on a leather seat.

Sam looked at Dean and immediately said, "Bobby's house, 2013."

Dean looked to Cas, "You know what to do, Cas." He turned to Sam, "This TARDIS is a bit battered and bruised at the moment so you might want to hold on, this is not going to be like Dad's."

Sam held on to the rail behind the seat he sat in as he watched Castiel and Dean slave over the controls. There were supposed to be six people manning the TARDIS but with two you had work twice as hard. Dean had a foot on the panel, pushing a lever down, both of his hands punching in numbers. Castiel had both of his feet on the panel and one hand on a button, the other arm was busy supporting his entire weight. Sam felt like he should help the struggling pair but he just sat still like a sack of potatoes.

The TARDIS engine started and the entire air craft shook. Sam held on for dear life as he watched Dean and Cas jump off the control panels on to floor with a grace in which they had not possessed only moments before. They grabbed the pillar for support as the TARDIS made rattling noises and groaned. This was only temporary as Dean pushed a button and the ship came to a bumpy stop, throwing Sam onto the floor.

Groggily Sam rose to his feet. He wondered how badly the TARDIS had been broken and how long Dean and Cas have been trying to fix it.

Dean checked Castiel to see if he was okay before running over to pick Sam up and check him over properly.

That was probably the worst landing that Dean had ever done in his life, but the terrain was too bumpy for a smooth landing.

"Everyone okay?" Dean asked, wanting to make sure no-one was in need of regeneration.

A sharp nod came from Cas, and a groan came from Sam.

Satisfied with his work, he wiped the pie off his face and went outside into the front yard of Bobby's house. Castiel followed quickly with a sick feeling Sam.

Once outside, Sam threw up.

Grimacing, Dean left the sick where it was and carried on through to the front porch supporting his sick brother.

He knocked on the door three times.

"Bobby!" Dean yelled, "It's me and Cas… Sam isn't feeling too good. My baby's a bit battered. I was wondering if you could help us fix her up."

The door opened a crack.

Dean looked and saw a disgruntled Bobby with his rifle.

"Its four in the morning, kid. What do you think you're playing at? Come in any way, sorry for all the clutter…" Bobby greeted them with less enthusiasm than they had hoped.

"Stupid Time Lords and their messed up sense of time…" he muttered under his breath.

"There is food in the kitchen and you can each take your respective bedrooms, Castiel, stay with Dean, Sam can take the upstairs bedroom. No funny business. Now I'm going back to bed. We can talk in the morning." Bobby grumbled a bit more and took Sam upstairs.

Dean turned to Cas, "Look, I don't know about you but I'm gonna hit the hay," he yawned, his hand coming up to cover his mouth, "you coming?"

Cas nodded, yawning with Dean, as they retired to the bed room.

Castiel took off his black shoes, trench coat and tie, unbuttoning the top buttons of his shirt. Dean just took off his shoes and jacket.

Dean got into the bed and got comfortable. Cas got in shortly after and they fell asleep side by side.

**A/N hope you enjoyed the first instalment, the next one shall be up by tomorrow. Please REVIEW! **

**Please have a look at Politically Incorrect by ImpalaTardis and look out for Dean's Journal. **


	2. Chapter 2

**A/N sorry for the late update, I had family stuff to do then I started school up again and we had a small exam the next day so I spent the day I was going to write it revising. But any way enjoy, leave a review and please check out Politically Incorrect a SuperWhoLock by me and my cousin ImpalaTardis (btw the epilogue is going to have you in stitches! ****) **

**Please enjoy and please leave a review XD**

Sam awoke on an unfamiliar bed. He was disorientated for a moment before the memories of the night before came rushing back.

He had sick all over his jumper and his long hair was stuck up in all the wrong places. Time Travel sickness was not a good look on Sam Winchester.

He looked at the clock beside him- 8:13am.

That meant it was the morning, well he thought it did.

He rose sleepily from the soft bed and rubbed the sleepy dust from his eyes.

He tried to rise up.

Immediately a headache hit him and he fell back on to the soft bed groaning. Today could begin tomorrow. He did have ten regenerations left so he might as well sleep; he had the time.

* * *

Dean woke up next to an upright Castiel. Concern brushed his face for a brief moment but was quickly hidden so as not to alarm Castiel; he was very good at reading people.

He tapped Castiel on the shoulder and he turned around slowly.

"Did you get any sleep last night, Cas?" Dean asked with a concerned facial expression.

He got a reluctant shake of the head.

He ruffled Castiel's hair as he got up out of the other side of bed and slowly walked around to Cas. He lowered his body so he was at eye level then rested his arms on the other's knees.

"You will get past this." Dean said reassuringly, lifting Castiel's head, which was looking forlornly at the floor. Dean sighed after he got no response from his friend and got up, leaving Castiel's head to flop back into its original position. He then moseyed to the door frame, putting on his signature grin, and in the cheeriest voice any one could muster in the morning, he questioned , "You know what wakes me up in the morning?"

"Pie?" Cas replied as he decided to play along with Dean's antics, plastering a fake smile on his face and getting off the bed.

"Bingo! You know me so well," Dean started," Help me find some then. I know Bobby has one somewhere around here…"

He faltered off and meandered to the kitchen with a less than eager Castiel trailing behind him.

Dean opened the fridge in a casual manor and peered inside, scrutinising the contents. Curiously he poked a foil covered object and recoiled quickly as it appeared to be squidgy. He looked over to Cas, who was barely holding in a giggle, and scowled. He dove back into the refrigerator again and poked another tinfoil covered object (with more caution this time) and smiled when it seemed like it had the same feel as pie. He took the foil off the object and recoiled again, it was mouldy pie. The smell stank out the kitchen.

Holding his nose, he disposed of the offending object in the bin and turned to Cas who was standing with a real smile placed on his lips.

"So my discomfort causes you to smile, eh. I just hope that I don't have to find mouldy food every time I want to cheer you up." Dean joked, but it just lowered the mood of the room as the reality of the statement sunk in.

He tried to apologise," Cas, I'm sor-"

"No don't, I understand it was a joke." Castiel interjected gloomily.

Just at that moment a confused Sam walked into the room.

The stench hit him.

"Eugh! What _is_ that?!" Sam exclaimed holding his nose to stop try and stop the revolting smell assault his nostrils.

Dean sheepishly looked at his shoes, "I was just trying to find pie! I didn't know it was mouldy!" he apologised taking the blame, "You look _awful_! Is that sick down your top…? Anyway," he continued, "How are you?"

Sam pulled a glass out of the cupboard; he went to the sink and filled it up and took a big gulp, "Fine, now. I think I was a bit dehydrated. I forgot to fix myself a drink of water before I left home." He explained, taking a smaller sip of the water.

Dean nodded and fiddled with his hands, Cas did likewise.

"Now we wait for Bobby to get up and we can fix my Baby!" Dean called out in the middle of the awkward silence which inevitably ensued.

* * *

Bobby awoke two hours later and after one more hour of finding the three hungry Gallifreyans something to eat, they were back on course to fix the TARDIS.

Dean led the foursome into the boughs of the TARDIS; that's where the problem was. It was further than any of the boys had gone before. Even when Dean decided to go exploring the day he received it from his father. They passed an assortment of different coloured doors, stairs and tunnels before finally reaching the room they required.

The door was rusty and the hinges were seized up. Obviously they could unlock the door with the screwdriver, but it was getting the door to actually open that was the real problem.

"How are we going to do this, eh boys. We're going to have to do the old push and shove. It shouldn't be a problem with you guys around." Bobby motioned for Dean to come over and he placed his hands by the handle. Bobby did the same.

"On three we push, okay…? One… two… three!"

Dean and Bobby strained against the door and leaned on it with all their body strength. There was hardly any grip on the floor and Dean would have almost fallen flat on his face if it weren't for Sam pushing him up every few seconds.

After ten minutes of getting know where, Sam offered some of his help, "Want some help there guys?"

A grunt of defiance came the answer.

"Suit yourself then." Sam pouted then sat on the wall by the door fiddling with the bottom of his shirt, which was still covered in sick.

Dean and Bobby gave one last push and in a flurry of dust they stumbled in to the '_Engine Room'_.

Everyone stared.

The '_Engine Room_' was full of tunnels of varying width with wires running through them at different points connecting them to each other in a giant web. But that wasn't what was so amazing. The centre piece was an obviously broken but beautiful orb. It had a blue hue emanating from its centre and a mix of sapphire and gold around the edges of it. It was almost perfectly round, except for a small crack running over the top of it.

"Enough staring, boys, we shall be able to fix it in a heartbeat." Bobby explained exasperatedly, shoving the boys through the door hole.

Dean didn't move, he just kept on staring at the orb, "It's my Baby's heart."

Bobby face palmed and sarcastically said, "Of course it is, boy. Now let's get on with it."

Bobby grabbed Dean's screwdriver from out of his pocket (ignoring the protests which came from Dean's mouth) and walked up to the gleaming orb. He hummed, scratching his head for a moment before his face lit up and he just pointed the screw driver at the crack and the crack vanished.

"More often than not, you can use the screwdriver to fix your TARDIS. It's common knowledge, Dean. If you actually concentrated when I was explaining how you would fix her without any tools, you'd know." Bobby chastised, hitting Dean on the head.

He cradled the back of his neck with a hurt expression on his face.

His face was then lost in thought, it then lit straight back up.

"Oh, I remember! I was eating the pie that Ellen had baked for me…" He trailed off as he felt Bobby stare into the depths of his soul.

Castiel shifted nervously, "What room is this? When I was growing up we were never allowed this far back." Castiel explained.

Bobby scratched his head in thought, "I don't kn-"

BOOM!

A huge crash was heard from the back of the room.

On instinct, Sam fled from the scene, leaving Bobby, Castiel and Dean.

Bobby swore as something nicked his shin and fell to the floor. He opened up the leg of his trousers and saw a huge gash, flowing with blood. He swore again.

"That looks bad..." Dean started, looking at the injury before turning to Castiel and ordered, "Get Bobby to the medical room and spray him up. When you've done that get Sam and hide in one of the storage rooms in case it's something dangerous. I'll find out what made the crash, but in case it is something dangerous you better move now."

Castiel looked like he was going to interrupt but another deafening crash sent him into action as even more shrapnel headed their way.

Dean cast off his plaid shirt to use as a makeshift bandage and tied it tightly around Bobby's leg. Cas then picked Bobby up with a grunt and they slowly made progress to the door.

With one last look at his best friend, Dean grimaced and covertly moved towards the source of the racket.

He hid around the side of the orb, before peaking around the side of it.

He blanched.

* * *

"Come on, only a few more corridors left," said Cas breathlessly, encouraging Bobby, who was falling over every two steps.

"Shut- Shut up, I c-can get th-th-there you know. I'm not gone yet," Bobby said unconvincingly, stumbling at an uneven bit of flooring.

Castiel sighed and continued lugging Bobby's big frame through the TARDIS.

He could still hear the noise coming from the heart of the TARDIS and all he wanted to do was run back and help, but Bobby was in danger of bleeding to death.

Sam looked for a way to the Control Panel, and in finding that, the way out. He had to get away from it. He didn't even feel guilty about leaving his brother, Castiel and Bobby in danger.

He walked quickly down a flight of stairs, he didn't remember going up a flight of stairs on the way to the '_Engine Room'_, but he knew that it was away from the noises and away from the memories.

He walked past Storage Room 1, and continued to walk. He knew there were about thirty storage rooms so if he went to the last one he would be hidden away enough so that any attacker couldn't find him.

He walked down another flight of stairs.

Storage Room Two passed him.

Another flight of stairs.

Storage Room Three passed him.

Another flight of stairs.

It continued like that until he had made his way to Storage Room Thirty in the theoretical dungeon of the TARDIS.

He peered through the porthole at the top of the door. All he could see were boxes and oddly shaped instruments. Deciding it was safe he opened the door and walked inside.

The door slammed shut behind him.

He jumped.

A figure jumped up and grabbed him around the middle. It dragged him to the back of the room kicking and screaming.

* * *

Castiel laid Bobby on the bed of the Medical Room and un-did the makeshift bandage placed on the wound. He sighed a sigh of relief- the bleeding had almost stopped.

Bobby lifted his head up to look at it, but was pushed back down by Castiel's strong arms.

"I've seen worse, you idjit." He grumbled in annoyance, clenching his fists as Castiel probed the cut.

"I know, but I need you to be still while I put the healing spray on and then you need to be still for an hour until it heals enough so that you can walk." Castiel sprayed the healing spray on, ignoring protests and abuse from his patient.

"It is not polite to do that when someone is healing you." Castiel stated, looking in Bobby's eyes with a piercing look of disapproval, "And stay still for an hour. I will go and get Sam."

Castiel left the room, leaving behind a grumpy Bobby.

* * *

Dean flew across the room and landed in a heap at the doorway. He barely managed to get back up before a creature with supernatural strength clutched his throat and pushed him against the door.

The creature before him had sharp pointed teeth which protruded out of its cheek when its mouth was closed and pointed outwards when its mouth was open, it gave I the appearance of bull dog ; they even had a yellowish glow. Its eyes bulged out of its head and the pupils were small slits that widened ever so slightly when the light was low. The creature was also extremely lanky in its posture and had a hunched back (hence Dean had already given it the nick name of Quasi Modo). It had claws on its hands about half a foot long and it had one big long claw on each of its big toes, like a velociraptor. It skin was a dark green.

"What an ugly son of-"

"Don't speak to Garserrath, like that…" The creature, now named Garserrath, hissed with its raspy voice, like metal scraping metal.

"What?" Dean murmured under his breath, hands grabbing on to its slimy arms, trying to relieve the pressure on his neck.

"Garserrath gets very angry when Time Lords talk to him like that… Wouldn't want anything to happen to your brother now do we…?" the alien had a monotonous voice.

Dean struggled against his attacker even more so when it mentioned his brother.

"Garserrath is just here to let Dean know that Dean's TARDIS is not safe anymore. Garserrath is not here to kill. Garserrath is here to warn."

* * *

Castiel found the Control Panel a little over half an hour later. He considered travelling to his home planet, Gallifrey, to ask for help, but the machine might not make it in one piece.

Was it worth taking them there for help and risking losing the TARDIS forever?

No, after Dean was done with whatever was in the '_Engine Room' _he would come and kill him personally, or stop him regenerating.

He walked around the Control Panel, wondering if he could ask for help from there, or ask for Sam's whereabouts, but a strange scratching noise was heard outside the TARDIS door and he was too curious to leave it alone thinking that it could be help, but that was highly unlikely.

He cautiously went to the door and looked out. It was normal. Nothing weird was going on.

He walked to go around the back of the TARDIS to see if the scratching was coming from elsewhere.

When he then walked back to the front of the TARDIS, the door closed on him, making him jump.

He tried pulling on the handle. He tried using his keys. He tried pushing on the door. He tried kicking the door down, but he could not get in. Crying out in anguish he sat down outside the door and sighed.

* * *

Bobby had guessed it had been over an hour and gingerly shifted his legs so they were hanging of the side of the bed. He then got up on his good foot and then put his other foot down slowly. He put pressure on it and when it didn't hurt he took a step forward. When that didn't hurt, he made it to the door.

He tried to open the door but it had somehow locked. He wanted to kick it down but he feared it could injure his leg further. Even though the spray healed the injury sufficiantly, it could not fully heal a big injury like that in under a day.

Cursing loudly he sunk on to the bed and ran his hand over his head.

What had these boys gotten themselves into?

**A/N I hope you like the next instalment, go check out Politically Incorrect by my cousin Impala Tardis and if it's not too inconvenient and please leave a review if you can XD**


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